Heparan sulfate modified proteins affect cellular processes central to neurodegeneration and modulate presenilin function.

Mutations in presenilin-1 (PSEN1) are the most common cause of familial, early-onset Alzheimer's disease (AD), typically producing cognitive deficits in the fourth decade. A variant of APOE, APOE3 Christchurch (APOE3ch) , was found associated with protection from both cognitive decline and Tau accumulation in a 70-year-old bearing the disease-causing PSEN1-E280A mutation. The amino acid change in ApoE3ch is within the heparan sulfate (HS) binding domain of APOE, and purified APOEch showed dramatically reduced affinity for heparin, a highly sulfated form of HS. The physiological significance of ApoE3ch is supported by studies of a mouse bearing a knock-in of this human variant and its effects on microglia reactivity and Aß-induced Tau deposition. The studies reported here examine the function of heparan sulfate-modified proteoglycans (HSPGs) in cellular and molecular pathways affecting AD-related cell pathology in human cell lines and mouse astrocytes. The mechanisms of HSPG influences on presenilin- dependent cell loss and pathology were evaluated in Drosophila using knockdown of the presenilin homolog, Psn , together with partial loss of function of sulfateless (sfl) , a homolog of NDST1 , a gene specifically affecting HS sulfation. HSPG modulation of autophagy, mitochondrial function, and lipid metabolism were shown to be conserved in cultured human cell lines, Drosophila , and mouse astrocytes. RNAi of Ndst1 reduced intracellular lipid levels in wild-type mouse astrocytes or those expressing humanized variants of APOE, APOE3 , and APOE4 . RNA-sequence analysis of human cells deficient in HS synthesis demonstrated effects on the transcriptome governing lipid metabolism, autophagy, and mitochondrial biogenesis and showed significant enrichment in AD susceptibility genes identified by GWAS. Neuron-directed knockdown of Psn in Drosophila produced cell loss in the brain and behavioral phenotypes, both suppressed by simultaneous reductions in sfl mRNA levels. Abnormalities in mitochondria, liposome morphology, and autophagosome-derived structures in animals with Psn knockdown were also rescued by simultaneous reduction of sfl. sfl knockdown reversed Psn- dependent transcript changes in genes affecting lipid transport, metabolism, and monocarboxylate carriers. These findings support the direct involvement of HSPGs in AD pathogenesis.

Measurement-guided volumetric dose reconstruction for helical tomotherapy.

It was previously demonstrated that dose delivered by a conventional linear accelerator using IMRT or VMAT can be reconstructed - on patient or phantom datasets - using helical diode array measurements and a technique called planned dose perturbation (PDP). This allows meaningful and intuitive analysis of the agreement between the planned and delivered dose, including direct comparison of the dose-volume histograms. While conceptually similar to modulated arc techniques, helical tomotherapy introduces significant challenges to the PDP formalism, arising primarily from TomoTherapy delivery dynamics. The temporal characteristics of the delivery are of the same order or shorter than the dosimeter's update interval (50 ms). Additionally, the prevalence of often small and complex segments, particularly with the 1 cm Y jaw setting, lead to challenges related to detector spacing. Here, we present and test a novel method of tomotherapy-PDP (TPDP) designed to meet these challenges. One of the novel techniques introduced for TPDP is organization of the subbeams into larger subunits called sectors, which assures more robust synchronization of the measurement and delivery dynamics. Another important change is the optional application of a correction based on ion chamber (IC) measurements in the phantom. The TPDP method was validated by direct comparisons to the IC and an independent, biplanar diode array dosimeter previously evaluated for tomotherapy delivery quality assurance. Nineteen plans with varying complexity were analyzed for the 2.5 cm tomotherapy jaw setting and 18 for the 1 cm opening. The dose differences between the TPDP and IC were 1.0% ± 1.1% and 1.1% ± 1.1%, for 2.5 and 1.0 cm jaw plans, respectively. Gamma analysis agreement rates between TPDP and the independent array were: 99.1%± 1.8% (using 3% global normalization/3 mm criteria) and 93.4% ± 7.1% (using 2% global/2 mm) for the 2.5 cm jaw plans; for 1 cm plans, they were 95.2% ± 6.7% (3% G/3) and 83.8% ± 12% (2% G/2). We conclude that TPDP is capable of volumetric dose reconstruction with acceptable accuracy. However, the challenges of fast tomotherapy delivery dynamics make TPDP less precise than the IMRT/VMAT PDP version, particularly for the 1 cm jaw setting.

ClariVein mechanochemical ablation: background and procedural details.

OBJECTIVES: The 2 primary objectives of this publication are to provide a practical step-by-step procedure for the ClariVein system and a focused literature review of endovenous ablation. MATERIALS AND METHODS: The ClariVein system is the first venous ablation technique to employ a hybrid (dual-injury) technique built into 1 catheter-based delivery system. Endomechanical abrasion is produced by the tip of the catheter's rotating wire (mechanical component); and endovenous chemical ablation (EVCA) is via simultaneous injection of sclerosant over the rotating wire (chemical component). The author is an early adopter of this technique and via experience has developed a detailed step-by-step protocol. DISCUSSION: To date, there have been 2 pivotal clinical studies published using the ClariVein system. These data are compared with the results using other methods of endovenous ablation. CONCLUSIONS: The ClariVein system is an exciting addition to the phlebologist's toolbox and has the potential to become a first-line treatment.

Validation of Pinnacle treatment planning system for use with Novalis delivery unit.

For an institution that already owns the licenses, it is economically advantageous and technically feasible to use Pinnacle TPS (Philips Radiation Oncology Systems, Fitchburg, WI) with the BrainLab Novalis delivery system (BrainLAB A.G., Heimstetten, Germany). This takes advantage of the improved accuracy of the convolution algorithm in the presence of heterogeneities compared with the pencil beam calculation, which is particularly significant for lung SBRT treatments. The reference patient positioning DRRs still have to be generated by the BrainLab software from the CT images and isocenter coordinates transferred from Pinnacle. We validated this process with the end-to-end hidden target test, which showed an isocenter positioning error within one standard deviation from the previously established mean value. The Novalis treatment table attenuation is substantial (up to 6.2% for a beam directed straight up and up to 8.4% for oblique incidence) and has to be accounted for in calculations. A simple single-contour treatment table model was developed, resulting in mean differences between the measured and calculated attenuation factors of 0.0%-0.2%, depending on the field size. The maximum difference for a single incidence angle is 1.1%. The BrainLab micro-MLC (mMLC) leaf tip, although not geometrically round, can be represented in Pinnacle by an arch with satisfactory dosimetric accuracy. Subsequently, step-and-shoot (direct machine parameter optimization) IMRT dosimetric agreement is excellent. VMAT (called "SmartArc" in Pinnacle) treatments with constant gantry speed and dose rate are feasible without any modifications to the accelerator. Due to the 3 mm-wide mMLC leaves, the use of a 2 mm calculation grid is recommended. When dual arcs are used for the more complex cases, the overall dosimetric agreement for the SmartArc plans compares favorably with the previously reported results for other implementations of VMAT: gamma(3%,3mm) for absolute dose obtained with the biplanar diode array passing rates above 97% with the mean of 98.6%. However, a larger than expected dose error with the single-arc plans, confined predominantly to the isocenter region, requires further investigation.

Cropland carbon fluxes in the United States: increasing geospatial resolution of inventory-based carbon accounting.

Net annual soil carbon change, fossil fuel emissions from cropland production, and cropland net primary production were estimated and spatially distributed using land cover defined by NASA's moderate resolution imaging spectroradiometer (MODIS) and by the USDA National Agricultural Statistics Service (NASS) cropland data layer (CDL). Spatially resolved estimates of net ecosystem exchange (NEE) and net ecosystem carbon balance (NECB) were developed. The purpose of generating spatial estimates of carbon fluxes, and the primary objective of this research, was to develop a method of carbon accounting that is consistent from field to national scales. NEE represents net on-site vertical fluxes of carbon. NECB represents all on-site and off-site carbon fluxes associated with crop production. Estimates of cropland NEE using moderate resolution (approximately 1 km2) land cover data were generated for the conterminous United States and compared with higher resolution (30-m) estimates of NEE and with direct measurements of CO2 flux from croplands in Illinois and Nebraska, USA. Estimates of NEE using the CDL (30-m resolution) had a higher correlation with eddy covariance flux tower estimates compared with estimates of NEE using MODIS. Estimates of NECB are primarily driven by net soil carbon change, fossil fuel emissions associated with crop production, and CO2 emissions from the application of agricultural lime. NEE and NECB for U.S. croplands were -274 and 7 Tg C/yr for 2004, respectively. Use of moderate- to high-resolution satellite-based land cover data enables improved estimates of cropland carbon dynamics.

Shipboard trials of an ozone-based ballast water treatment system.

Legislation introduced by the United Nations International Maritime Organization (IMO) has focused primarily on standards defining successful treatments designed to remove invasive species entrained in ballast water. An earlier shipboard study found that ozone introduced into salt water ballast resulted in the formation of bromine compounds, measured as total residual oxidants (TRO) that were toxic to both bacteria and plankton. However, the diffuser system employed to deliver ozone to the ballast water tanks resulted in patchiness in TRO distribution and toxicity to entrained organisms. In this follow-up study, the shipboard diffuser system was replaced by a single Venturi-type injection system designed to deliver a more homogeneous biocide distribution. Within-tank variability in TRO levels and associated toxicity to zooplankton, phytoplankton and marine bacteria was measured via a matrix of tubes deployed to sample different locations in treated and untreated (control) tanks. Three trials were conducted aboard the oil tanker S/T Prince William Sound in the Strait of Juan de Fuca off Port Angeles, Washington State, USA, between June and December 2007. Mortalities of plankton and bacteria and oxidant concentrations were recorded for treated and untreated ballast water up to 3days following treatment, and residual toxicity beyond this period was measured by bioassay of standard test organisms. Results indicated uniform compliance with current IMO standards, but only partial compliance with other existing and pending ballast water legislation.

Skin dose study of chest wall treatment with tomotherapy.

PURPOSE: The tangential-beam technique frequently presents challenges in homogeneity of radiation dose to the target. To ensure an adequate dose to the skin, a bolus is often used. Tomotherapy has already been shown to improve target conformity and homogeneity in other disease sites. Because of the tangential delivery technique and lack of flattening filter in TomoTherapy accelerators, we hypothesize that during chest wall irradiation using tomotherapy, the skin dose will be adequate without bolus. MATERIALS AND METHODS: This study compares the dosimetric differences between tomotherapy chest wall irradiation and traditional linear accelerator-based tangential-beam technique. Tomotherapy treatment plans with and without bolus were compared with tangentialbeam plans. Plans were also generated for phantom studies, and point doses were measured using MOSFET dosimetry to verify the adequate skin dose. Monte Carlo simulations of static beams of both techniques were performed, and dosimetry was compared. RESULTS: Monte Carlo simulations and measurements confirmed that beams from tomotherapy deliver a higher skin dose than a standard linear accelerator. Skin dose also increases with the incident angle of the beams. CONCLUSION: Because of the characteristics of the tomotherapy beam and delivery technique, chest wall treatment plans from tomotherapy showed adequate skin dose [more than 75% of prescribed planning target volume (PTV) dose] even without bolus.

Insights into palladium-catalyzed cyanation of bromobenzene: additive effects on the rate-limiting step.

Kinetic studies using reaction calorimetry were conducted under synthetically relevant conditions to study the effect of additives in the cyanation of bromobenzene catalyzed by palladium complexes. This work demonstrates that the addition of a catalytic amount of ZnBr(2) facilitates the reaction with an elimination of the induction period observed without additive. This study afforded a qualitative assessment of the effect of water on the rate-limiting step and the apparent reaction order in bromobenzene.

Microbial hydroxylation of o-bromophenylacetic acid: synthesis of 4-substituted-2,3-dihydrobenzofurans.

Microbial hydroxylation of o-bromophenylacetic acid provided 2-bromo-5-hydroxyphenylacetic acid. This enabled a route to the key intermediate 4-bromo-2,3-dihydrobenzofuran for synthesizing a melatonin receptor agonist and sodium hydrogen exchange compounds. Pd-mediated coupling reactions of 4-bromo-2,3-dihydrobenzofuran provided easy access to the 4-substituted-2,3-dihydrobenzofurans.

Peptide-based in vitro assay for the detection of reactive metabolites.

We describe a novel peptide-based in vitro method for the detection of reactive metabolites that is amenable for use with microsomal or purified enzyme systems. Covalently bound adducts are detected by mass spectrometry using a surface-enhanced laser desorption ionizationtime of flight detector. The trapping molecule is an 11 amino acid peptide (ECGHDRKAHYK) that contains cysteine and other nucleophilic amino acid residues, as well as charged residues to enhance binding to a weak cation exchange chip surface used with the detection system. The assay concept was initially tested using rat or human liver microsomes with a series of benzodioxolanes. The assay was refined using human recombinant cytochrome P450 3A4 as the bioactivation system and validated with a series of positive and negative reference compounds. Alternative individual human recombinant P450 enzymes (e.g., 1A1, 2C9, or 2D6) may be used in place of 3A4 as the bioactivation system, or several P450 enzymes can be combined together into a single bioactivation system. We found that a mixture of P450s 3A4, 2C9, and 2D6 was suitable as a rapid general screen for the detection of reactive metabolites that covalently bind to proteins. Combining results from assays of individual P450 enzymes with microsomal systems allows the rapid profiling of metabolic pathways involved in reactive metabolite generation and provides valuable information that can be used to guide structural modifications to minimize the potential for metabolic bioactivation. In addition, non-P450 enzymes may be used as activation systems, such as peroxidases or alcohol dehydrogenase. In summary, this peptide-based assay system is able to detect reactive metabolites generated from a structurally diverse set of drugs and xenobiotics using a variety of microsomal or purified enzyme activation systems.

Remarkable beta-selectivity in the synthesis of beta-1-C-arylglucosides: stereoselective reduction of acetyl-protected methyl 1-C-arylglucosides without acetoxy-group participation.

An efficient and practical process to generate beta-C-arylglucoside derivatives was achieved. The process described involves Lewis acid mediated ionic reduction of a peracetylated 1-C-aryl methyl glucoside derived from the addition of an aryl-Li to selectively protected delta-D-gluconolactone. The reduction of the 2-acetoxy-1-C-oxacarbenium ion intermediates proceeds with a high degree of selectivity to give beta-C-arylglucosides without 2-acetoxy group participation. Furthermore, during the reduction process we also identified an unprecedented critical role of water. By changing from the usual benzyl ether protecting groups because of cost and chemical compatibility concerns, the new process is made additionally efficient and highly selective.

First-generation agents: aspirin, heparin and coumarins.

Aspirin, heparin and the coumarins are the classical anti-thrombotic agents. They represent the platform upon which newer drugs holding the promise of greater efficacy and less toxicity are being developed. Even as such newer drugs arrive into clinical practice, the older agents remain remarkable for their decades-long pre-eminence. All derive from natural sources, and none from a search for therapeutic anti-thrombotic agents; they have saved countless lives but also served as essential probes into basic mechanisms of thrombosis. Testament to their clinical importance is that these agents are the only drugs profiled on a regular basis in special scientific statements by the American Heart Association/American College of Cardiology and by the American College of Chest Physicians. This chapter reviews their biology, uses and limitations.

CT venography in suspected pulmonary thromboembolism.

Pulmonary embolism (PE) and deep venous thrombosis (DVT) are a continuum and are difficult to diagnose clinically. Combined CT venography and pulmonary angiography (CTVPA) is a single examination that combines multidetector CT pulmonary angiography (CTPA) and CT venography (CTV) of the abdomen, pelvis, and lower extremities, providing "one-stop shopping" for venous thromboembolism without additional venipuncture or i.v. contrast, and it adds only a few additional minutes to scanning time. CTVPA rapidly and accurately examines the deep veins, reveals the presence, absence, and extent of deep venous thrombosis, serves as a baseline, and helps guide patient management. Multiple investigators have reported a high degree of accuracy when CTV is compared with venous ultrasound. There are some pitfalls in image interpretation, especially with regard to mixing artifacts, and there are continuing controversies as to exactly which parts of the abdomen, pelvis, and legs should be scanned routinely, the ideal timing of CTV acquisition relative to contrast injection, and the slice thickness and gap, if any, that should be used.

A multiple in silico program approach for the prediction of mutagenicity from chemical structure.

We have conducted an evaluation of three of the most widely used commercial toxicity prediction programs, Toxicity Prediction by Komputer Assisted Technology (TOPKAT), Deductive Estimation of Risk from Existing Knowledge (DEREK) for Windows (DfW) and CASETOX. The three programs were evaluated for their ability to predict Ames test mutagenicity using 520 proprietary drug candidate (Test set 1) and 94 commercial (Test set 2) compounds. The study demonstrates that these three commercially available programs are useful, with limitations in their ability to predict mutagenicity over a wide range of chemical space, i.e. global predictivity. Individually, each of the programs performed at an acceptable level for overall accuracy, i.e. the ability to predict the correct outcome. However, analysis of the predictions indicates that the overall accuracy figure is heavily weighted by the ability of the programs to correctly predict non-mutagens, whereas none of the programs individually performed well in the prediction of novel mutagenic structures, i.e. Ames positive compounds. The performance of these programs' in predicting Ames positive mutagens appeared to be independent of the chemical utility of the compound, i.e. industrial, agricultural or pharmaceutical. The combination of program predictions provided some improvement in overall accuracy, sensitivity and specificity.

Efficient asymmetric synthesis of the vasopeptidase inhibitor BMS-189921.

[reaction: see text] An efficient asymmetric synthesis of the vasopeptidase inhibitor BMS-189921 was accomplished. Two short enantioselective syntheses of the common key intermediate (S)-alpha-aminoazepinone 6b were developed. Olefin 3 was converted to 6b via asymmetric hydrogenation. Alternatively, enyne 12 was converted to racemic alpha-aminoazepinone 15b, which was transformed to 6b by a practical dynamic resolution.

Role of predictive metabolism and toxicity modeling in drug discovery--a summary of some recent advancements.

In this article, we discuss recent advances and selected publications in the area of computer-based (in silico) metabolism and toxicity prediction, and comment on the opportunities for prediction of metabolism-based toxicity. The article also discusses the growing interest and importance of in silico prediction of metabolism and toxicity as tools to assist in library design and lead optimization. In addition, we consider the status of commercial metabolism and toxicity databases, and the need for future improvement, since data is often from older studies and from structures not typically considered as 'drug-like'. The article highlights the current status and potential of in silico models for property prediction, and the potential for linkage with vivo models to improve the integration of metabolism and toxicity into the drug discovery process and extrapolation to clinical studies. The article underscores that the future development, integration and application of in silico models will require a balance of local and global model approaches. The article also indicates that implementation and integration of models into drug discovery processes needs to be carried out in a rational and systematic manner, if we are to fully capitalize on the opportunity presented by in silico predictive modeling.

Combined CT venography and pulmonary angiography: a comprehensive review.

The combination of computed tomographic (CT) venography and pulmonary angiography (CTVPA) was initially described in 1998 as a single comprehensive noninvasive imaging examination for suspected thromboembolic disease. It allowed the identification of pulmonary embolism as well as deep venous thrombosis (DVT) in the abdomen, pelvis, thighs, and calves. The venographic portion of CTVPA has now been studied by multiple researchers and has been shown to be an accurate imaging study for the thigh veins in comparison with lower extremity sonography. In contrast to sonography, however, CTVPA readily and rapidly permits evaluation of the inferior vena cava, the pelvic veins, the calf veins, and all of the superficial venous system. Complex venous anatomy can be surveyed, an additional sonographic study is not required, and only a few extra minutes and images are required over and above CT pulmonary angiography. A review of 957 recent cases of suspected pulmonary embolism examined with CTVPA revealed an overall 10.5% frequency of DVT, with a nearly equal distribution of thrombosis at the common femoral, superficial femoral, popliteal, and deep calf veins. Although a variety of protocols for CTVPA may be implemented, including a contiguous helical acquisition, obtaining 5- or 10-mm-thick images every 4 cm provides a high degree of accuracy and decreases overall radiation dose.